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BTFS_BRD

Mathematical Methods
Contact Hours /Week
Total Lecture Hours
Total Tutorial Hours
Sub. Code

: 3 Hrs.
:40
:0
:
:BRD01

Module-I

Credits
CIE Marks
SEE Marks

2011

:4
: 50
: 50

07 Hrs

Introduction: Scope of biostatistics, definition, data collection, presentation of data, graphs,


charts (scale diagram, histogram, frequency polygon, frequency curve, logarithmic curves).
Sampling & selection bias, probability sampling, random sampling, sampling designs.
Descriptive statistics: Measure of central tendency (arithmetic mean, geometric mean, harmonic
mean, median, quartiles, mode); Measure of dispersion (range, quartile deviation, mean deviation
and standard deviation, coefficient of variation).
Module-II

08 Hrs

Bi-Variate Distribution: Correlation and regression analysis (simple and linear) curve fitting
(linear, non-linear and exponential).
Probability: Axioms, models, conditional probability, Bayes rule, Genetic Applications of
Probability, Hardy - Weinberg law, Wahlund's Principle, Forensic probability determination,
Likelihood of paternity, Estimation of probabilities for multilocus/ multi-allele finger print
systems.
Module-III

08Hrs.

Statistical Inference: Estimation theory and testing of hypothesis, point estimation, interval
estimation, sample size determination, simultaneous confidence intervals, parametric and nonparametric distributions (T-test, F-test, Chi Squared distribution, goodness of fit test) analysis of
variance (one-way and two-way classifications). Case studies of statistical designs of biological
experiments (RCBD, RBD).

BTFS_BRD

Module-IV

2011

07 Hrs.

Probability Distributions: Discrete probability distributions - Binomial, Poisson, geometric


derivations. Central limit theorem. Continuous probability distribution normal, exponential,
gamma distributions, beta and Weibull distributions, T & F distributions.
Design of Experiments: Sample surveys, comparisons groups and randomization, random
assignments, single and double blind experiments, blocking and extraneous variables, limitations
of experiments.
Case Studies: Cigarette smoking, Lung cancer, endangered plants species, epidemics.
Module-V

Problems for module I-IV

TEXT BOOKS
1 Wayne W Daniel

Biostatistics, Wiley 7th Edition

2 Ronadd N Forthofer and Eun Sul Lee

Introduction to Biostatistics, Academic Press.

3 Norman T J Bailey

Statistical methods in Biology, Cambridge Press.

4 J.N.Kapur.

Mathematical Models in Biology and Medicine

5 Ipsen, Feigl & Bancroff

Introduction to Biostatistics

6 Animesh K Datta

Basic Biostatistics & its Applications

7 Lehninger

Principles of Biochemistry

BTFS_BRD

2011

BASIC BIOINFORMATICS AND DATABASE MANAGEMENT


Contact
Week
Total
Hours

Hours/ : 04
Lecture : 52

Sub. Code

: (BRD02)

Credits :

CIE Marks :

50

SEE Marks :

50

Module-I
Introduction to Biological databases
Bioinformatics: (What is Bioinformatics, Goals, Scope, Application, Limitations and New
Themes).Database: (What is a database, Types) Biological Database: Databases (Primary,
Secondary and Specialized), Interconnection between the databases, Fit falls of Biological
databases. Nucleotide and Protein sequence databases (NCBI, Genbank, EMBL, DDBJ, PDB
and MMDB) Format of databases GenBank flat file, FASTA Format, PIR Format)
10 Hours.
Module-II
Sequence Alignment and Database Similarity Searching
Sequence Alignment: Evolutionary Basis, Homology versus Similarity, Similarity versus
Identity, Global alignment, Local alignment, Pairwise alignment,
Alignment algorithm:
Scoring Matrices: Amino acid scoring matrices; PAM, BLOSUM, Comparison between PAM
and BLOSUM, Statistics of Sequence Alignment (e-Value, p-value)
Database Similarity Searching: BLAST. BLAST variants. Statistical significance. Low
complexity Regions. BLAST output format. FASTA. Simple Alignment problems. Sequence
alignment algorithms : DOT Matrix Dynamic programming algorithm: Comparative Genomics
and proteomics ,Heuristic similarity searches: FASTA, BLAST, BLAT.

BTFS_BRD

Module-III

2011

10 Hours.

Motif, Domain and Gene Prediction


Scoring Function , exhaustive algorithms, Heuristic algorithms, practical issues. Profiles and
Hidden Markov Models: PSSM. Profiles. Markov Model and HMM. Zeroth, First and Higher
order HMM. Protein Motif and Domain Prediction: Identification of Motif and Domains in
MSA. PROSITE. Motif and Domain Databases using Statistical Models ( PRINTS, BLOCKS,
ProDom, Pfam, SMART)Protein Family databases ( COG). Motif Discovery and Sequence
Logos. Numerical conceptual on 0th 1st and Higher order HMM.
11 Hours
Module-IV
Molecular Phylogenetics and Protein structure visualization: Phylogenetics Basics, classification
(Maximum likelihood and parsimony method). Terminologies, Gene versus species phylogeny,
Forms of tree representation. Tree Construction: Choosing Molecular Markers. Alignment.
Multiple Substitutions. DISTANCES, GROW TREE PAUP, PHYLIP. Choosing Substitution
Models (Jukes Cantor Model).
Protein structural visualization: Rasmol, Swiss-PDB viewer, Chime, Cn3D. Protein structure
comparison: Intermolecular, Intramolecular and combined methods. Multiple structure
alignment. Protein structure classification: SCOP and CATH, Secondary structure Prediction: Ab
Initio Methods, Secondary structure Prediction for transmembrane proteins: Helical membrane
proteins, RNA structure prediction.
Module-V
Other Databases

11 Hours

Introduction, Purpose of Database systems


Chemical compound databases (PubChem, NCI, ZINC, Drug Bank, Ligand)
Other Important Databases: KEGG, Pubmed, OMIM, Medline, TIGR. BioMed Central, Public
Library of Sciences (PloS), CiteXplore.

BTFS_BRD

2011

TEXT BOOKS:
1.

Andreas D Baxevanis

Bioinformatics, Wiley Interscience, 1998.

2.

David W Mount

Bioinformatics, Cold spring

3.

Jin Xiong

Essentials Bioinformatics, Cambridge University Press

arbour, 2001.

REFERENCE BOOKS:
1.

R F Doolittle

Computational methods for macromolecular sequence analysis,


Academic Press, 1996.

2.

S C Rastogi, N
Mendiratta & P Rastogi,

Bioinformatics, Methods and Applications- Genomics,


Proteomics and Drug, Discovery Phi, 2006.

3.

Arthur Lesk

Introduction to Bioinformatics, Oxford, 2006.

4.

Stuart M Brown

Bioinformatics, NYU Medical Center, NY USA. 2000.

5.

Middha Sk, T. Usha &

Bioinformatics, CBH Publishers, 2012

Prashanth HP

BTFS_BRD

Molecular Modeling and Drug design


Contact Hours /Week
: 3 Hrs.
Total Lecture Hours
:40
:0
Total Tutorial Hours
:0
Sub. Code
:BRD 03

Credits
CIE Marks
SEE Marks

Module I

2011

:3
: 50
: 50

07 Hours.

Principles of protein structure; Hierarchical organization of protein structure Primary.


Secondary, Super secondary, Tertiary and Quaternary structure; Hydrophobicity of amino acids,
van der Waal and Solvent accessible surface, Internal coordinates of proteins; Derivation,
significance and applications of Ramachandran Map, protein folding.
Protein structure prediction : basic principles of protein structure, first-principles methods for
predicting protein structure, motifs of protein structure, alpha domain structures, alpha/beta
structures, folding and flexibility, prediction, engineering and design of protein structures.
MODULE II

8 Hours.

Insilco Drug Design and Computer Assisted New Lead Design:


Introduction, historical perspective, drug compounds, reparation and organization for drug
seeking, common stages in the drug seeking campaign, sources of hits, leads and candidate
drugs, Natural products: higher plant and animal products, combinational libraries, Lead
optimization. Introduction, Basic Concepts, Molecular Recognition by Receptor and Ligand
Design, Active Conformation, Approaches to Discover New Functions, Approaches to the Cases
with known and unknown receptor structure. Introduction to drug metabolism, toxicity and
pharmacokinetics, toxicology considerations, problems and drawbacks on drug discovery and
development.
MODULE III

09 Hours

Molecular Modelling and Simulation:


Introduction of molecular modelling Coordinate system, Potential energy surfaces, Molecular
modelling Literature, steps in molecular modelling: introduction to Quantum Mechanics,
introduction to Molecular mechanics. Force filed, Types of force filed.
Example: Amber force filed, CHARMM force filed.
Introduction to Van der Waals interaction, Hydrogen bonding in molecular mechanics,
Model for Molecular simulations, introduction about molecular dynamics.
MODULE IV

07 Hours

BTFS_BRD

2011

Structure Prediction and Drug Design


Drug design and discovery: an overview. Protein Structure Prediction - Introduction to
Comparative Modelling. Sequence Alignment. Constructing and Evaluating a Comparative
Model. Predicting Protein Structures by 'Threading, Comparative between Homology Modelling
and Threading,
Basics of molecular modelling, methods, steps involved in MM, Selection of target and template,
homology modelling, refinement and validation-SAVES Server, The Critical Assessment of
protein Structure Prediction (CASP), Superposition of proteins using different tools, RMSD,
Presentation of protein conformations, Hydrophobicity factor, Shape complementary
Molecular Docking studies, Structure based De Novo Ligand design, Drug Discovery - QSAR.
Module- V
Molecular Docking and case studies:
Different types of docking approaches (Structure based, Ligand based)
ADMET properties of drug, Lipinski Rules of 5
Docking and Virtual Screening: Using different docking algorithms, Optimization of docking
algorithms based on different target (protein and DNA),Virtual screening-High throughput
screening of Drugs, Post docking analysis, Mode of interaction studies, Pharmacophore
prediction based on the docking analysis.
Computer-assisted drug design/Structural drug design:
Case studies (Any two or three)
Aplaviroc: CCR5 receptor antagonists
Capsazepine: TRPV1 antagonists
TEXT BOOKS

Celecoxib:Cyclooxygenase 2 inhibitors
Darunavir:HIV protease inhibitors

Povl Krogsgaard and


Larsen

Molecular modelling, I edition, Multivista Global


Ltd.2002.

Andrew R Leach

Molecular modelling: principles and applications, 2nd


edition, Pearson education ltd., 2001.

Reference Books:
1. A.R.Leach, Molecular Modelling Principles and Application, Longman, 1996.
2. J.M.Haile, Molecular Dynamics Simulation Elementary Methods, John Wiley and Sons, 1997.
3. Satya Prakash Gupta, QSAR and Molecular Modeling, Springer - Anamaya Publishers, 2008

BTFS_BRD

Computer Languages and Network Informatics


Contact Hours /Week
: 4 Hrs.
Credits
Total Lecture Hours
:40
CIE Marks
SEE Marks
Sub. Code
:BRD04

Module I

2011

:4
: 50
: 50

07 Hrs

Computer design of oligonucleotide probes:Introduction, Oligonucleotide probe design


methodology, filtering of low-complexity sequence: RepeatMasker, prediction of cross
hybridization to related genes, thermodynamics of nucleic acid duplexes and the prediction of
melting temperature, probe secondary structure: computation of probe secondary structure,
Mfold over the web.
Image processing: Introduction, Feature extraction: identifying the position of the feature,
identifying the pixels that comprise the feature, identifying the background pixels.
Module II
Normalization: Introduction, Data cleaning and Transformation: removing flagged features,
background subtraction, logarithms. Within array normalization: linear regression of Cy5 against
Cy3, linear regression of log ratio against average intensity, non-linear regression of log ratio
against average intensity, correcting for spatial effects. Measuring and quantifying microarray
variability: Introduction, measuring and quantifying microarray variability: calibration
experiments, pilot studies, quantifying the variability, log-normal distribution, methods for
measuring the variability, variation between replicate features on the array, variability between
hybridizations to different arrays, variability between the individuals.
Analysis of differentially expressed genes: Introduction, fundamental concepts: statistical
inference, hypothesis tests, p-values, independence, classical parametric statistics: one sample ttest, two sample t-test, requirement of t-test, non-parametric statistics: bootstrap analysis
Module III
Computer concepts : Introduction to digital computer: Basic functional units of a digital
computer central processing unit, Arithmetic and Logic unit, control unit, Memory unit, Input
and Output units, Stored Program concept, Types of computer.

BTFS_BRD

2011

Storage devices Primary storage: Random access memory, Read only Memory, Secondary
storage Floppy disk, Hard disk, CD- ROM and its operation.
Computer Language Machine language, Assembly language and assembler, High-level
languages and compiler, Interpreter, Editor. System software, Application software.
Algorithm and Flow charts: The meaning of algorithms / flowcharts and their need, Example
Algorithms and Flowcharts.
Module IV

07 Hrs

History & Evolution of Java ,Overview of Java ,Data Types, Variables, and Arrays , Operators ,
Control statements ,Introducing Classes , A Closer Look at Methods and Classes , Inheritance
Packages and Interfaces , Exception Handling , Multithreaded Programming , Enumerations,
Autoboxing, and Annotations (Metadata) , I/O, Applets, and Other Topics
Module V

08 Hrs

Biojava: sequence input, sequence output etc


Bioperl: Introduction to Perl, Unix basics, Sequences and Strings Variables, Arrays,Files ,Motifs
and Loops ,Flow control ,String operators ,Writing files .
Introduction to Biopython, General overview of what Biopython provides , working with
sequences , and usage example.

Dov Stekel

Microarray Bioinformatics first edition, Cambridge university press,


2005.

Mark Schena

Microarray Analysis new edition, J. Wiley & Sons, 2002.

C programming

Balguruswamy

James Tisdall

Beginning Perl for Bioinformatics

Herbert Schildt

Java The Complete reference

BTFS_BRD

Computer Languages and Network Informatics


Contact Hours /Week
: 4 Hrs.
Credits
Total Lecture Hours
:40
CIE Marks
:0
SEE Marks
Sub. Code
:BRDL01

2011

:4
: 50
: 50

LAB 1
Part A: BASICS OF BIOINFORMATICS AND SEQUENCE LAB
1. Sequence retrieval from nucleic acid and protein databases
2. Sequence (FASTA and BLAST) searches Analysis of parameters affecting alignment.
3. Pair wise comparison of sequences Analysis of parameters affecting alignment.
4. Multiple alignments of sequences Analysis of parameters affecting alignment.
5. Evolutionary studies / Phylogenetic analysis Analysis of parameters affecting trees.
6. Identification of functional sites in Genes / Genomes.
7. Secondary structure prediction of proteins.
8. Pattern elucidation in Proteins (PROSITE).
9. Primer Design.
10. Structure analysis using Rasmol and pymol
11. Comparative Modeling of homologous sequences.
12. Superposition of structures Calculation of RMSD for main chain atoms.
Part B :
Lab name and objective(s) of the lab
1. Protein Structure Retrieval and Visualization
2. Active site Prediction Using Online server & Free tools
3. Active site Prediction Using Commercial software
4. Protein Minimization - CHARMm forcefield using
5. Ligand Retrieval and Visualization
6. To check Lipinski rule and ADMET Properties for small molecules
7. Ligand Minimization CHARM and MMF forcefield
8. Molecular Docking using Free tool
9. Molecular Docking Using Commercial software
10. Visualization and Analysis of Docking Result
11. Homology Modeling
12. Creating and validating a 3D QSAR Pharmacophore

10

BTFS_BRD

Computer Languages and Network Informatics lab


Contact Hours /Week
: 4 Hrs.
Credits
Total Lecture Hours
:40
CIE Marks
:0
SEE Marks
Sub. Code
:BRDL02

2011

:4
: 50
: 50

Programming using PERL and BioPERL.


1. Storing and retrieving amino acid sequences using structure data types
2. Swapping two values using pointers
3. File Processing Creation and simple processing
4. Computing amino acid composition of a given protein sequence.
Web Publishing
1. User interface design
2. Create a web page for your University / College using HTML - The opening page should
provide hyperlinks to other
pages (add animation and sound effects appropriately).
3. Creating a web page to get protein sequence data and compute and display amino acid
composition
4. Creating a web page to get nucleic acid sequence data and compute and display base
composition.
BASIC OPERATIONS IN MATLAB AND R

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